<p>The amount of livestock wastewater is increasing worldwide, leading to increasing ammonia contamination in both surface water and groundwater. Therefore, it is crucial to treat ammonia effectively to mitigate this growing environmental issue. This study aimed to utilize the bacteria in natural soil for the biological elimination of ammonia from wastewater, focusing on evaluating the removal mechanisms. The first batch experiment assessed ammonia removal via nitrification and adsorption using natural soil and artificial wastewater, while the second batch experiment focused on evaluating ammonia removal efficiency through adsorption alone. In the third and fourth batch experiments, samples were taken and analyzed for bacterial activity and ammonia nitrogen isotope composition. Ammonia nitrogen isotope data were interpreted using the Rayleigh fractionation model. The reduction of ammonia observed in this study was attributed to nitrification, adsorption, and volatilization, contributing approximately 29%, 33%, and 38% to the overall reduction, respectively. The phylum <i>Proteobacteria</i>, known for its role in both nitrification and denitrification processes, dominated throughout the study period. The enrichment factor associated with ammonia nitrification in this study ranged from −13.2‰ to −66.4‰, while that for ammonia adsorption ranged from −33.2‰ to −54.1‰. The enrichment factor for nitrification also accounts for the potential influences of slight volatilization and adsorption. This study demonstrates that natural soil possesses inherent capabilities to effectively reduce ammonia levels in wastewater. By elucidating the differences in reaction mechanisms between bacterial nitrification and physical adsorption, this study has the potential to significantly advance ammonia removal techniques in wastewater treatment.</p>